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R
Python
Git/GitHub
Bash
docker

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Made with the R packages datadrivencv and pagedown.

The source code is available on github.com/dzhang32/cv.

Last updated on 2022-03-24.

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David Zhang

Experienced bioinformatician who enjoys learning and applying the best practices for method development. I focus on developing robust, user-friendly tools that harness transcriptomic data to improve the rate of genetic diagnosis.

Education

PhD, Bioinformatics

University College London

London, UK

Present - 2017

  • Thesis: Using transcriptomics to improve the genetic diagnosis rate of rare disease patients.

MSc, Neuroscience

University College London

London, UK

2016 - 2015

  • Thesis: The role of mitochondrial dysfunction in Xerodoma pigmentosum
  • Grade: Merit (68%)
  • Awarded post-graduate support scheme bursary (£10,000)

BSc, Biomedical science

University College London

London, UK

2015 - 2012

  • Thesis: Investigating the function of CYFIP1 in the development of rat hippocampal neurons.
  • Grade: 2:1 (69%)

H.S.

Queen Elizabeth’s School

Barnet, UK

2012 - 2007

  • Grades: Maths (A*), Biology (A*), Chemistry (A*), Sociology (A).



Work Experience

Bioinformatician internship (2 months)

Verge Genomics

Remote, US

2021

  • Goal: Set up an aberrant splicing detection pipeline for drug target discovery in C9orf72 ALS patients.
  • Used docker to setup a reproducible workflow for running aberrant splicing analyses on an AWS instance.

Research Technician

University College London

London, UK

2017 - 2016

  • Goal: Investigate the impact of genetic variation on the age of onset of dementia and cognition within Down syndrome patients.



Software & programming

Bioconductor packages

N/A

N/A

Present - 2020

  • dasper: Detection of aberrant splicing events in RNA-sequencing. Author and maintainer.
  • megadepth: BigWig and BAM related utilities. An R wrapper for the megadepth software developed by Chris Wilks. Co-author and maintainer.
  • ODER: Optimising the definition of Expressed Regions. Submitted to Bioconductor. Co-author and maintainer.

R packages

N/A

N/A

Present - 2022

  • ggtranscript: Visualising transcript structure and annotation using ggplot2. Author and maintainer.
  • autorecipes: Automate your recipe planning. Author and maintainer.

Python packages

N/A

N/A

Present - 2021

  • autogroceries: Automate your grocery shop. Author and maintainer.
  • codino converts a codon design to the expected amino acid frequencies, and vice versa. Author and maintainer.

Web scraping

N/A

N/A

2021

  • Applied the python packages Beautiful Soup and Selenium to web scrape information on all UK biotechnology companies.

Data science blog

N/A

N/A

2021

  • Chess-related blog post was selected for the hand-on-tutorials column in Towards Data Science, which displays pieces that highlight best practices of data science.
  • Applied popular data science packages in python to analyse chess.com data.



Teaching Experience

Developing Bioconductor packages

University College London

Virtual Event

2020

  • Hosted workshop on best practices for developing Bionconductor packages using biocthis.

R package development

Rstats club

Virtual Event

2020

  • Presentation about unit testing fundamentals, the importance of testing and new features released in the R package testthat edition 3.
  • Presentation about pre-commit hooks in R.
  • Presentation about the best practices of developing R packages.

R fundamentals

Clinician Coders

London, UK

2020 - 2018

  • Developed materials and lead workshops that aimed to teach R fundamentals to clinicians.

RNA-sequencing for diagnostics

Kings College London

London, UK

2020 - 2017

  • Lectured graduate level students about how transcriptomics can be applied in the diagnostic pipeline.

Selected Publications

recount3: summaries and queries for large-scale RNA-seq expression and splicing

Genome Biology

N/A

2021

  • Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B
  • Role: Adviser.
  • DOI: https://doi.org/10.1186/s13059-021-02533-6

Developmental Consequences of Defective ATG7-Mediated Autophagy in Humans

The New England Journal of Medicine

N/A

2021

  • Collier J, Guissart C, Oláhová M, Sasorith S, Piron-Prunier F, Suom Fi, Zhang D, Martinez-Lopez N, Leboucq N, Bahr A, Azzarello-Burri S, Reich S, Schöls L, Polvikoski TM, Meyer P, Larrieu L, Schaefer AM, Alsaif HS, Alyamani S, Zuchner S, Barbosa IA, Deshpande C, Pyle A, Rauch A, Synofzik M, Alkuraya FS, Rivier F, Ryten M, McFarland R, Delahodde A, McWilliams TG, Koenig M, and Taylor RW.
  • Role: Analyst
  • DOI: https://doi.org/10.1056/NEJMoa1915722

Megadepth: efficient coverage quantification for BigWigs and BAMs

Bioinformatics

N/A

2021

Integration of eQTL and Parkinson’s disease GWAS data implicates 11 disease genes

Jama Neurology

N/A

2021

  • Kia DA, Zhang D, Guelfi S, Manzoni C, Hubbard L, United Kingdom Brain Expression Consortium (UKBEC), International Parkinson’s Disease Genomics Consortium (IPDGC), Reynolds RH, Botía JA, Ryten M, Ferrari R, Lewis PA, Williams N, Trabzuni D, Hardy J, Wood NW.
  • Role: Co-first author.
  • DOI: https://doi.org/10.1001/jamaneurol.2020.5257

Incomplete annotation of disease-associated genes is limiting our understanding of Mendelian and complex neurogenetic disorders.

Science advances

N/A

2020

  • Zhang D, Guelfi S, Ruiz SG, Costa B, Reynolds RH, D’Sa K, Liu W, Courtin T, Peterson A, Jaffe AE, Hardy J, Botia JA, Collado-Torres L and Ryten M.
  • Role: First Author.
  • DOI: https://doi.org/10.1126/sciadv.aay8299

Regulatory sites for known and novel splicing in human basal ganglia are enriched for disease-relevant information.

Nature Communications

N/A

2020

  • Guelfi S, D’Sa K, Botía J, Vandrovcova J, Reynolds RH, Zhang D, Trabzuni D, Collado-Torres L, Thomason A, Leyton PQ, Gagliano SA, Nalls MA, UK Brain Expression Consortium, Small KS, Smith C, Ramasamy A, Hardy J, Weale ME & Ryten M.
  • Role: Analyst.
  • DOI: https://doi.org/10.1038/s41467-020-14483-x

Genetic variability in response to Aβ deposition influences Alzheimer’s risk.

Brain Communications

N/A

2019

  • Salih DA, Bayram S, Guelfi S, Reynolds RH, Shoai M, Ryten M, Brenton JW, Zhang D, Matarin M, Botia JA, Shah R, Brookes KJ, Guetta-Baranes T, Morgan K, Bellou E, Cummings DM, Escott-Price V, Hardy J.
  • Role: Analyst.
  • DOI: https://doi.org/10.1093/braincomms/fcz022

Duplication of 10q24 locus: broadening the clinical and radiological spectrum.

Eur J Hum Genet

N/A

2019

  • Holder-Espinasse M, Jamsheer A, Escande F, Andrieux J, Petit F, Sowinska-Seidler A, Socha M, Jakubiuk-Tomaszuk A, Gerard M, Mathieu-Dramard M, Cormier-Daire V, Verloes A, Toutain A, Plessis G, Jonveaux P, Baumann C, David A, Farra C, Colin E, Jacquemont S, Rossi A, Mansour S, Ghali N, Moncla A, Lahiri N, Hurst J, Pollina E, Patch C, Ahn JW, Valat AS, Mezel A, Bourgeot P, Zhang D, Manouvrier-Hanu S.
  • Role: Analyst.
  • DOI: https://doi.org/10.1038/s41431-018-0326-9

Variation at the TRIM11 locus modifies Progressive Supranuclear Palsy phenotype.

Annals of Neurology

N/A

2018

  • Jabbari E, John W, Tan MMX, Maryam S, Pittman A, Ferrari R, Mok KY, Zhang D, Reynolds RH, de Silva R, Grimm MJ, Respondek G, Muller U, Al-Sarraj S, Gentleman SM, Lees AJ, Warner TT, Hardy J, Revesz T, Hoglinger GU, Holton JL, Ryten M and Morris HR.
  • Role: Analyst.
  • DOI: https://doi.org/10.1002/ana.25308



Conferences

The British Society for Genetic Medicine (BSGM)

N/A

Virtual Event

2021

  • Talk: dasper: detecting aberrant splicing events in RNA-sequencing data

EuroBioc

N/A

Virtual Event

2020

  • Talk: dasper: detecting aberrant splicing events in RNA-sequencing data

Genomics England Research Conference

N/A

London, UK

2019

  • Poster: Predicting disease-causing genes using machine learning

Genomics of Rare Disease

N/A

Cambridge, UK

2019

  • Poster: The use of transcriptomics to improve gene annotation
  • Poster: Using machine learning to understand and predict genes causing rare neurological disorders
  • Awarded prize for the best poster (£100)

International Parkinson’s Disease Genomics Consortium (IPDGC)

N/A

Lisbon, Portugal

2019

  • Talk: Incomplete annotation of disease-associated genes is limiting our understanding of Mendelian and complex neurogenetic disorders

European Society of human genetics (ESHG)

N/A

Milan, italy

2018

  • Poster: Incomplete annotation of OMIM genes is likley to be limiting the diagnostics yield from genetic tests.

International Parkinson’s Disease Genomics Consortium (IPDGC)

N/A

Reykjavik, Iceland

2018

  • Poster: Incomplete annotation of OMIM genes is limiting the diagnostic yield from genetic tests.

World Science Conference Israel (WSCI)

N/A

Jerusalem, Israel

2015

  • 1 of 11 UK participants chosen to attend.